Fine Mapping And Candidate Gene Analysis Of A Major QTL On SSC17 For Carcass Length In Duroc×Landrace×Yorkshire Crossbred Pigs

In pigs,body size is highy related to meat production and may affect the reproductive performance and disease susceptibility to a certainextent,therefore,body size is an economically important traits.Swine body size is mainly controlled by genetic factors and has moderate to high heritability?h²>0.5?.However,the current knowledge about the genetic mechanism of pig body size is still very limited.In this study,we firstly conducted genome-wide association analysis?GWAS?to identify quantitative trait locus?QTL?body length in duroc×landrace×large yorkshire?DLY?three-cross commercial pigs,then performed QTL fine mapping,candidate gene study and transcriptome analysis for the largest effect QTL on SSC17,in order to decipher the molecular mechanism underlying the QTL.Our laboratory has slaughtered more than 1200 DLY pigs in tow batches and measured their carcass traits.We used porcine 60k SNP chips to scan the first batch of 610DLY pigs and GWAS analysis revealed a total of eight significant SNPs(P<1 x 10^-5)associated with carcass straight length?CSL?and carcass diagonal length?CDL?which distribute on chromosome 14 and 17.The most significant SNP was ALGA0093437?P=1.64E-07?,located at 16.76 Mb on SSC17.On the SNP also represents the most significant locus influencing the total length of cervical spine,while show on effect the number of vertebrae,indicating that likely this locus influence the body length by regulating the growth of the vertebrae.Moreover,the QTL region also contains a significant association signals for carcass weight and body mass index?BMI?.We then verified the effect of the ALGA0093437 on the body length in the second batch of DLY.In order to refine the SSC17 QTL niterval,we selected 500 individuals with extreme phenotype from the whole population,and dexelopped 191 new SNPs within the QTL interval to genotype the selected samples.The regional association analysis identified to the most significant SNP sn3154?P=5.22E-23?,which has much higher significance than the original GWAS top SNP ALGA0093437.By using the LOD-4 drop-off method.the QTL confidence interval was restricted to 360kb range.At the SNP sn3154,the allele A showed a favorable effect and a dominant effect,because the CSL of pigs with AG and AA genotypes was 5⁸ cm longer than of pigs whit GG genotype.The frequencies of allele A in Duroc,Large White,Landrace and DLY were 0,0.038,0.781 and 0.22respectively.These results indicates that the QTL has a wide and important application potential for the molecular breeding of western commercial pig breeds.The QTL just reside a gene desert which contains only a BMP2 gene,This gene plays a role in promoting the formation of bone and cartilage,so it is a prime candidate gene.Comparative analysis of the full-length BMP2 gene sequences detected 56variants,including a missense mutation?g.11927 T>C?in an exon,The function of the missense mutation was predicted by the software tmhmm,The result showed that the structure and physicochemical properties of the protein were not altered due to the mutation.Moreover,the association between the SNP and the phenotype was not significant.so the missense mutation could be excluded as causal mutation underlying the QTL..To reveal the role of the QTL in regulation of skeletal development,we analysed transcriptome of cartilage tissues from 10 individuals of two groups consists of 5 pigs with long?short?CSL phenotype.A total of 20 differentially expressed genes?DEG?were indentified,including BMP2.GO?Gene Ontology?analysis indicated that the DEGs were mainly involued in the growth and development process,and the KEGG analysis also identified some significally enriched pathways,including TGF-beta pathway known to regulate chondrocyte proliferation and hypertrophic differentiation in embryonic bone cuttures.As BMP2 gene is a member of TGF super family,the result supports our speculation that BMP2 is a causal gene underlying the SSC17 QTL.This study greatly reduced the interval of QTL SSC17,initially identified BMP2 as a causal gene,and suggested that the QTL effect is associated with a regulatory rather than structural mutation in the BMP2 gene.